Duplication of part of the genome is known to occur via an RNA intermediate which is reverse-transcribed into complementary DNA (cDNA) by reverse transcriptase. For a review, see Weiner et al., Ann. Rev. Biochem., 55, 631 (1986). The consequential reverse flow of genetic information is considered to have played a major role in the evolutionary diversification of eukaryotic genomes. A similar mechanism may very well have been responsible for genomic evolution in procaryotes in the light of the recent discoveries of bacterial transcriptases. See Inouye and Inouye, TIBS, 16, 18 (1991a) and Inouye and Inouye, Ann. Rev. Microbiol., 45, 163 (1991b). Gene duplication through cDNA synthesis by reverse transcriptase is believed to have played an important role in diversification of genomes during evolution.
The invention arose in connection with basic research related to genome evolution. The synthesis of a unique ss-slDNA during plasmid DNA replication was demonstrated. It may be speculated that slDNA production may be widely prevalent during both procaryotic as well as eucaryotic chromosomal DNA replication. The chromosomal genetic elements followed by IR structures may always be subject to duplication into slDNA at a frequency depending on the stability of the IR structure and the property of the polymerase(s).
It has been shown that there are many inverted repeat (IR) structures (approximately 1,000 copies in E. coli), known as REPs for repetitive extragenic palindromic sequences or PUs for palindromic units. Higgins et al., Nature, 298, 760 (1982), Gilson et al., EMBO. J., 3, 1417 (1984) and Gilson et al., Nucl. Acids Res., 19, 1375 (1991). These structures appear to be associated with specific cellular components including DNA polymerase 1, and may be playing a significant role in chromosomal organization. Gilson et al., Nucl. Acids Res. 18, 3941 (1990) and Gilson et al., EMBO. J., 3, 1417 (1984). It should also be noted that approximately 6% of the human genome are occupied with elements called Alu whose transcriptional products have been shown to contain substantial secondary structures. Simmett et al., J. Biol. Chem., 266, 8675 (1991).
Since slDNA synthesis does not require RNA intermediates nor reverse transcriptase activity in contrast to that of cDNA synthesis, slDNA may be more frequently produced than cDNA. Thus, slDNAs might have played a major role similar to cDNA in the genomic evolution of both procaryotes and eucaryotes by duplicating genetic elements which then were dispersed or rearranged within the genome.